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NGS-QC: A quality control system for profiles obtained ChIP Sequencing
As you certainly know data sets obtained by enrichment-based technologies coupled to massive parallel sequencing (ChIP-seq, DNase-seq, FAIRE-seq, GRO-seq, MeDIP-seq, MRE-seq, …) can vary significantly, even in cases where for example the same cell types and antibodies are used for ChIP-seq. The complexity of these assays, differences in conditions (crosslinking, chromatin shearing, …) and variation in experimenter manipulation are aspects that contribute to these apparent variation.
We would like to draw your attention to a QC system that is freely available to the academic community and will be described in a publication that that has just come out*. This system is composed of a tool (NGS-QC Generator) that generates Quality Control Indicators (QCis) and a database that comprises at present more than 5600 QCis for publicly available NGS data sets. We will further develop this tool and expand the database to ultimately harbour all enrichment-based NGS profiles.
The NGS-QC Generator computes numerical QCis and generates an extensive quality control report from the raw sequencing data set without the need of prior peak calling. This NGS-QC report relates the QCis for your profile relative to all 5600 datasets in the QCi database and calculates a QC-STAMP composed of three letters where AAA ('triple A') is the top quality.
With the QC analysis you will save time, as the NGS-QC Generator uses the raw data set. You can thus decide at an early time point to continue the analysis or optimize conditions. The NGS-QC report can also help you to choose a sequencing depth to use to obtain a certain quality level.
The NGS-QC Generator (customized Galaxy instance), the QC indicator database and a detailed Tutorial are available at
http://igbmc.fr/Gronemeyer_NGS_QC
We invite all users to share their experience in using these tools with us in the discussion forum available at the above site.
*M. A. Mendoza-Parra, W. Van Gool, M. A. Mohamed Saleem, D.G. Ceschin and H. Gronemeyer (2013) A quality control system for profiles obtained by ChIP-sequencing. Nucl. Acids Res 2013; doi: 10.1093/nar/gkt829. A PDF copy can be downloaded from
http://nar.oxfordjournals.org/cgi/re...zg&keytype=ref
Best regards,
The NGS-QC team of the Gronemeyer Lab
We would like to draw your attention to a QC system that is freely available to the academic community and will be described in a publication that that has just come out*. This system is composed of a tool (NGS-QC Generator) that generates Quality Control Indicators (QCis) and a database that comprises at present more than 5600 QCis for publicly available NGS data sets. We will further develop this tool and expand the database to ultimately harbour all enrichment-based NGS profiles.
The NGS-QC Generator computes numerical QCis and generates an extensive quality control report from the raw sequencing data set without the need of prior peak calling. This NGS-QC report relates the QCis for your profile relative to all 5600 datasets in the QCi database and calculates a QC-STAMP composed of three letters where AAA ('triple A') is the top quality.
With the QC analysis you will save time, as the NGS-QC Generator uses the raw data set. You can thus decide at an early time point to continue the analysis or optimize conditions. The NGS-QC report can also help you to choose a sequencing depth to use to obtain a certain quality level.
The NGS-QC Generator (customized Galaxy instance), the QC indicator database and a detailed Tutorial are available at
http://igbmc.fr/Gronemeyer_NGS_QC
We invite all users to share their experience in using these tools with us in the discussion forum available at the above site.
*M. A. Mendoza-Parra, W. Van Gool, M. A. Mohamed Saleem, D.G. Ceschin and H. Gronemeyer (2013) A quality control system for profiles obtained by ChIP-sequencing. Nucl. Acids Res 2013; doi: 10.1093/nar/gkt829. A PDF copy can be downloaded from
http://nar.oxfordjournals.org/cgi/re...zg&keytype=ref
Best regards,
The NGS-QC team of the Gronemeyer Lab